Biophotonic probes for bio-detection and imaging

Revolutionizing agriculture with nanotechnology: Innovative approaches in fungal disease management and plant health monitoring

Nanotechnology has emerged as a transformative force in modern agriculture, offering innovative solutions to address challenges related to fungal plant diseases and overall agricultural productivity. Specifically, the antifungal activities of metal, metal oxide, bio-nanoparticles, and polymer nanoparticles were examined, highlighting their unique mechanisms of action against fungal pathogens. Nanoparticles can be used as carriers for fungicides, offering advantages in controlled release, targeted delivery, and reduced environmental toxicity. Nano-pesticides and nano-fertilizers can enhance nutrient uptake, plant health, and disease resistance were explored. The development of nanosensors, especially those utilizing quantum dots and plasmonic nanoparticles, promises early and accurate detection of fungal pathogens, a crucial step in timely disease management. However, concerns about their potential toxic effects on non-target organisms, environmental impacts, and regulatory hurdles underscore the importance of rigorous research and impact assessments. The review concludes by emphasizing the significant prospects of nanotechnology in reshaping the future of agriculture but advocates for a balanced approach that prioritizes safety, sustainability, and environmental stewardship.

A comprehensive review on the biomedical frontiers of nanowire applications

This comprehensive review examines the immense capacity of nanowires, nanostructures characterized by unbounded dimensions, to profoundly transform the field of biomedicine. Nanowires, which are created by combining several materials using techniques such as electrospinning and vapor deposition, possess distinct mechanical, optical, and electrical properties. As a result, they are well-suited for use in nanoscale electronic devices, drug delivery systems, chemical sensors, and other applications. The utilization of techniques such as the vapor-liquid-solid (VLS) approach and template-assisted approaches enables the achievement of precision in synthesis. This precision allows for the customization of characteristics, which in turn enables the capability of intracellular sensing and accurate drug administration. Nanowires exhibit potential in biomedical imaging, neural interfacing, and tissue engineering, despite obstacles related to biocompatibility and scalable manufacturing. They possess multifunctional capabilities that have the potential to greatly influence the intersection of nanotechnology and healthcare. Surmounting present obstacles has the potential to unleash the complete capabilities of nanowires, leading to significant improvements in diagnostics, biosensing, regenerative medicine, and next-generation point-of-care medicines.

Lossy Mode Resonance Sensors Based on Anisotropic Few-Layer Black Phosphorus

Lossy mode resonance (LMR) sensors offer a promising avenue to surpass the constraints of conventional surface plasmon resonance (SPR) sensors by delivering enhanced label-free detection capabilities. A notable edge of LMR over SPR is its excitation potential by both transverse electric (TE) and transverse magnetic (TM) polarized light. Yet this merit remains underexplored due to challenges to achieving high sensing performance under both TM and TE polarization within a singular LMR model. This study introduces a theoretical model for an LMR prism refractive index sensor based on a MgF2-few layer black phosphorus-MgF2 configuration, which can achieve angular sensitivity nearing 90° refractive index unit-1 (RIU-1) for both polarizations. Leveraging the distinct anisotropic nature of black phosphorus, the figure of merit (FOM) values along its two principal crystal axes (zigzag and armchair) show great difference, achieving an impressive FOM of 1.178 × 106 RIU-1 along the zigzag direction under TE polarized light and 1.231 × 104 RIU-1 along the armchair direction under TM polarized light. We also provide an analysis of the electric field distribution for each configuration at its respective resonant conditions. The proposed structure paves the way for innovative applications of anisotropic-material-based LMR sensors in various applications.

Highly-Adaptable Optothermal Nanotweezers for Trapping, Sorting, and Assembling across Diverse Nanoparticles

Optical manipulation of various kinds of nanoparticles is vital in biomedical engineering. However, classical optical approaches demand higher laser power and are constrained by diffraction limits, necessitating tailored trapping schemes for specific nanoparticles. They lack a universal and biocompatible tool to manipulate nanoparticles of diverse sizes, charges, and materials. Through precise modulation of diffusiophoresis and thermo-osmotic flows in the boundary layer of an optothermal-responsive gold film, highly adaptable optothermal nanotweezers (HAONTs) capable of manipulating a single nanoparticle as small as sub-10 nm are designed. Additionally, a novel optothermal doughnut-shaped vortex (DSV) trapping strategy is introduced, enabling a new mode of physical interaction between cells and nanoparticles. Furthermore, this versatile approach allows for the manipulation of nanoparticles in organic, inorganic, and biological forms. It also offers versatile function modes such as trapping, sorting, and assembling of nanoparticles. It is believed that this approach holds the potential to be a valuable tool in fields such as synthetic biology, optofluidics, nanophotonics, and colloidal science.

Light-controlled soft bio-microrobot

Micro/nanorobots hold exciting prospects for biomedical and even clinical applications due to their small size and high controllability. However, it is still a big challenge to maneuver micro/nanorobots into narrow spaces with high deformability and adaptability to perform complicated biomedical tasks. Here, we report a light-controlled soft bio-microrobots (called "Ebot") based on Euglena gracilis that are capable of performing multiple tasks in narrow microenvironments including intestinal mucosa with high controllability, deformability and adaptability. The motion of the Ebot can be precisely navigated via light-controlled polygonal flagellum beating. Moreover, the Ebot shows highly controlled deformability with different light illumination duration, which allows it to pass through narrow and curved microchannels with high adaptability. With these features, Ebots are able to execute multiple tasks, such as targeted drug delivery, selective removal of diseased cells in intestinal mucosa, as well as photodynamic therapy. This light-controlled Ebot provides a new bio-microrobotic tool, with many new possibilities for biomedical task execution in narrow and complicated spaces where conventional tools are difficult to access due to the lack of deformability and bio-adaptability.

Nonlinear optical response of heme solutions

Heme is the prosthetic group for cytochrome that exists in nearly all living organisms and serves as a vital component of human red blood cells (RBCs). Tunable optical nonlinearity in suspensions of RBCs has been demonstrated previously, however, the nonlinear optical response of a pure heme (without membrane structure) solution has not been studied to our knowledge. In this work, we show optical nonlinearity in two common kinds of heme (i.e., hemin and hematin) solutions by a series of experiments and numerical simulations. We find that the mechanism of nonlinearity in heme solutions is distinct from that observed in the RBC suspensions where the nonlinearity can be easily tuned through optical power, concentration, and the solution properties. In particular, we observe an unusual phenomenon wherein the heme solution exhibits negative optical nonlinearity and render self-collimation of a focused beam at specific optical powers, enabling shape-preserving propagation of light to long distances. Our results may have potential applications in optical imaging and medical diagnosis through blood.

High Q-Factor Single-Mode Lasing in Inorganic Perovskite Microcavities with Microfocusing Field Confinement

The realization of high-Q single-mode lasing on the microscale is significant for the advancement of on-chip integrated light sources. It remains a challenging trade-off between Q-factor enhancement and light-field localization to raise the lasing emission rate. Here, we fabricated a zero-dimensional perovskite microcavity integrated with a nondamage pressed microlens to three-dimensionally tailor the intracavity light field and demonstrated linearly and nonlinearly (two-photon) pumped lasing by this microfocusing configuration. Notably, the microlensing microcavity experimentally achieves a high Q-factor (16700), high polarization (99.6%), and high Purcell factor (11.40) single-mode lasing under high-repetition pulse pumping. Three-dimensional light-field confinement formed by the microlens and plate microcavity simultaneously reduces the mode volume (∼3.66 μm3) and suppresses diffraction and transverse walk-off loss, which induces discretization on energy-momentum dispersions and spatial electromagnetic-field distributions. The Q factor and Purcell factor of our lasing come out on top among most of the reported perovskite microcavities, paving a promising avenue toward further studying electrically driven on-chip microlasers.

Stimuli-Responsive Polymer-Based Nanosystems for Cancer Theranostics

Stimuli-responsive polymers can respond to internal stimuli, such as reactive oxygen species (ROS), glutathione (GSH), and pH, biological stimuli, such as enzymes, and external stimuli, such as lasers and ultrasound, etc., by changing their hydrophobicity/hydrophilicity, degradability, ionizability, etc., and thus have been widely used in biomedical applications. Due to the characteristics of the tumor microenvironment (TME), stimuli-responsive polymers that cater specifically to the TME have been extensively used to prepare smart nanovehicles for the targeted delivery of therapeutic and diagnostic agents to tumor tissues. Compared to conventional drug delivery nanosystems, TME-responsive nanosystems have many advantages, such as high sensitivity, broad applicability among different tumors, functional versatility, and improved biosafety. In recent years, a great deal of research has been devoted to engineering efficient stimuli-responsive polymeric nanosystems, and significant improvement has been made to both cancer diagnosis and therapy. In this review, we summarize some recent research advances involving the use of stimuli-responsive polymer nanocarriers in drug delivery, tumor imaging, therapy, and theranostics. Various chemical stimuli will be described in the context of stimuli-responsive nanosystems. Accordingly, the functional chemical groups responsible for the responsiveness and the strategies to incorporate these groups into the polymer will be discussed in detail. With the research on this topic expending at a fast pace, some innovative concepts, such as sequential and cascade drug release, NIR-II imaging, and multifunctional formulations, have emerged as popular strategies for enhanced performance, which will also be included here with up-to-date illustrations. We hope that this review will offer valuable insights for the selection and optimization of stimuli-responsive polymers to help accelerate their future applications in cancer diagnosis and treatment.

First hyperpolarizability of the di-8-ANEPPS and DR1 nonlinear optical chromophores in solution. An experimental and multi-scale theoretical chemistry study

The solvent effects on the linear and second-order nonlinear optical properties of an aminonaphtylethenylpyridinium (ANEP) dye are investigated by combining experimental and theoretical chemistry methods. On the one hand, deep near infrared (NIR) hyper-Rayleigh scattering (HRS) measurements (1840-1950 nm) are performed on solutions of di-8-ANEPPS in deuterated chloroform, dimethylformamide, and dimethylsulfoxide to determine their first hyperpolarizablity (βHRS). For the first time, these HRS experiments are carried out in the picosecond regime in the deep NIR with very moderate (≤3 mW) average input power, providing a good signal-to-noise ratio and avoiding solvent thermal effects. Moreover, the frequency dispersion of βHRS is investigated for Disperse Red 1 (DR1), a dye commonly used as HRS external reference. On the other hand, these are compared with computational chemistry results obtained by using a sequential molecular dynamics (MD) then quantum mechanics (QM) approach. The MD method allows accounting for the dynamical nature of the molecular structures. Then, the QM part is based on TDDFT/M06-2X/6-311+G* calculations using solvation models ranging from continuum to discrete ones. Measurements report a decrease of the βHRS of di-8-ANEPPS in more polar solvents and these effects are reproduced by the different solvation models. For di-8-ANEPPS and DR1, comparisons show that the use of a hybrid solvation model, combining the description of the solvent molecules around the probe by point charges with a continuum model, already achieves quasi quantitative agreement with experiment. These results are further improved by using a polarizable embedding that includes the atomic polarizabilities in the solvent description.

Recent Advances in Biosensor Development for the Detection of Viral Particles in Foods: A Comprehensive Review

Viral foodborne diseases cause serious harm to human health and the economy. Rapid, accurate, and convenient approaches for detecting foodborne viruses are crucial for preventing diseases. Biosensors integrating electrochemical and optical properties of nanomaterials have emerged as effective tools for the detection of viruses in foods. However, they still face several challenges, including substantial sample preparation and relatively poor sensitivity due to complex food matrices, which limit their field applications. Hence, the purpose of this review is to provide an overview of recent advances in biosensing techniques, including electrochemical, SERS-based, and colorimetric biosensors, for detecting viral particles in food samples, with emerging techniques for extraction/concentration of virus particles from food samples. Moreover, the principle, design, and advantages/disadvantages of each biosensing method are comprehensively described. This review covers the recent development of rapid and sensitive biosensors that can be used as new standards for monitoring food safety and food quality in the food industry.

The molecular mechanism of non-covalent inhibitor WU-04 targeting SARS-CoV-2 3CLpro and computational evaluation of its effectiveness against mainstream coronaviruses

There is an urgent need for highly effective therapeutic agents to interrupt the continued spread of SARS-CoV-2. As a pivotal protease in the replication process of coronaviruses, the 3CLpro protein is considered as a potential target of drug development to stop the spread and infection of the virus. In this work, molecular dynamics (MD) simulations were used to elucidate the molecular mechanism of a novel and highly effective non-covalent inhibitor, WU-04, targeting the SARS-CoV-2 3CLpro protein. The difference in dynamic behavior between the apo-3CLpro and the holo-3CLpro systems suggests that the presence of WU-04 inhibits the motion amplitude of the 3CLpro protein relative to the apo-3CLpro system, thus maintaining a stable conformational binding state. The energy calculations and interaction analysis show that the hot-spot residues Q189, M165, M49, E166, and H41 and the warm-spot residues H163 and C145 have a strong binding capacity to WU-04 by forming multiple hydrogen bonds and hydrophobic interactions, which stabilizes the binding of the inhibitor. After that, the resistance of WU-04 to the six SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Lambda, and Omicron) and two other mainstream coronavirus (SARS-CoV and MERS-CoV) 3CLpro proteins was further investigated. Excitingly, the slight difference in energy values relative to the SARS-CoV-2 system indicates that WU-04 is still highly effective against the coronaviruses, which becomes crucial evidence that WU-04 is a pan-inhibitor of the 3CLpro protein in various SARS-CoV-2 variants and other mainstream coronaviruses. The study will hopefully provide theoretical insights for the future rational design and improvement of novel non-covalent inhibitors targeting the 3CLpro protein.

Humanoid-shaped WaveFlex biosensor for the detection of food contamination

High-toxicity secondary metabolites called aflatoxin are naturally produced by the fungus Aspergillus. In a warm, humid climate, Aspergillus growth can be considerably accelerated. The most dangerous chemical among all aflatoxins is aflatoxin B1 (AFB1), which has the potential to cause cancer and several other health risks. As a result, food forensicists now urgently need a method that is more precise, quick, and practical for aflatoxin testing. The current study focuses on the development of a highly sensitive, specific, label-free, and rapid detection method for AFB1 using a novel humanoid-shaped fiber optic WaveFlex biosensor (refers to a plasmon wave-based fiber biosensor). The fiber probe has been functionalized with nanomaterials (gold nanoparticles, graphene oxide and multiwalled carbon nanotubes) and anti-AFB1 antibodies to enhance the sensitivity and specificity of the developed sensor. The findings demonstrate that the developed sensor exhibits a remarkable low detection limit of 34.5 nM and exceptional specificity towards AFB1. Furthermore, the sensor demonstrated exceptional characteristics such as high stability, selectivity, reproducibility, and reusability. These essential factors highlight the significant potential of the proposed WaveFlex biosensor for the accurate detection of AFB1 in diverse agricultural and food samples.

Stimulated-responsive refractive-diffractive biological hydrogel micro-optical element enabling achromatism via femtosecond laser lithography

Herein, we report a novel biological hydrogel-based achromatic refractive-diffractive micro-optical element with single-material apochromatism. Benefiting from the stimulated responsive property of the hydrogel, pH modulation yielded swelling and affected the refractive index of the element, enabling multi-wavelength focusing performance tuning and chromatic aberration adjustment. Using femtosecond laser lithography, we fabricated a separate hydrogel microlens and Fresnel zone plate and measured the tunable focusing performance while varying pH; the results were consistent with our simulation results. Furthermore, we designed and fabricated a hydrogel-based achromatic refractive-diffractive micro-optical element and demonstrated achromatism with respect to three wavelengths using only one material consisting of a microlens and a Fresnel zone plate. We characterized the optical focusing properties and observed smaller chromatic aberration. The potential applications of such hybrid microoptical elements include biomedical imaging and optical biology sensing.

Bio-inspired optical structures for enhancing luminescence

Luminescence is an essential signal for many plants, insects, and marine organisms to attract the opposite sex, avoid predators, and so on. Most luminescent living organisms have ingenious optical structures which can help them get high luminescent performances. These remarkable and efficient structures have been formed by natural selection from long-time evolution. Researchers keenly observed the enhanced luminescence phenomena and studied how these phenomena happen in order to learn the characteristics of bio-photonics. In this review, we summarize the optical structures for enhancing luminescence and their applications. The structures are classified according to their different functions. We focus on how researchers use these biological inspirations to enhance different luminescence processes, such as chemiluminescence (CL), photoluminescence (PL), and electroluminescence (EL). It lays a foundation for further research on the applications of luminescence enhancement. Furthermore, we give examples of luminescence enhancement by bio-inspired structures in information encryption, biochemical detection, and light sources. These examples show that it is possible to use bio-inspired optical structures to solve complex problems in optical applications. Our work will provide guidance for research on biomimetic optics, micro- and nano-optical structures, and enhanced luminescence.

Flexible waveguide integrated thermo-optic switch based on TiO2 platform

Mechanically flexible photonic devices are critical components of novel bio-integrated optoelectronic and high-end wearable systems, in which thermo-optic switches (TOSs) as optical signal control devices are crucial. In this paper, flexible titanium oxide (TiO₂) TOSs based on a Mach-Zehnder interferometer (MZI) structure were demonstrated around 1310 nm for, it is believed, the first time. The insertion loss of flexible passive TiO₂ 2 × 2 multi-mode interferometers (MMIs) is -3.1 dB per MMI. The demonstrated flexible TOS achieves power consumption (Pπ) of 0.83 mW, compared with its rigid counterpart, for which Pπ is decreased by a factor of 18. The proposed device could withstand 100 consecutive bending operations without noticeable degradation in TOS performance, indicating excellent mechanical stability. These results provide a new perspective for designing and fabricating flexible TOSs for flexible optoelectronic systems in future emerging applications.

A biophotonic device based on a conjugated polymer and a macrophage-laden hydrogel for triggering immunotherapy

A biophotonic device is fabricated by a 3D printing technique for tumor immunotherapy utilizing a flexible organic light-emitting diode (OLED) with deep blue emission and a gelatin-alginate hydrogel that contains a poly(phenylene vinylene) (PPV) derivative and live immune cells of macrophages (M₀-RAW264.7). PPV is excited by the OLED to generate reactive oxygen species (ROS), enabling the macrophages to polarize to the M₁ phenotype and secrete cytotoxic cytokines to induce the apoptosis of tumor cells. This strategy provides a new method for fabricating cell-involved biophotonic devices for immunotherapy.

Point-of-care optical devices in clinical imaging and screening: A review on the state of the art

Integration of optical technologies in biomedical sciences permitted light manipulation at smaller time-length scales for specific detection and imaging of biological entities. Similarly, advances in consumer electronics and wireless telecommunications strengthened the development of affordable and portable point-of-care (POC) optical devices, circumventing the necessity of conventional clinical analyses by trained personnel. However, many of the POC optical technologies translated from bench to bedside require industrial support for their commercialization and dissemination to the population. This review aims to demonstrate the intriguing progress and challenges of emerging POC devices utilizing optics for clinical imaging (depth-resolved and perfusion imaging) and screening (infections, cancer, cardiac health, and haematologic disorders) with a focus on research studies over the previous 3 years. Special attention is given to POC optical devices that can be utilized in resource-constrained environments.

Wake-Riding Effect-Inspired Opto-Hydrodynamic Diatombot for Non-Invasive Trapping and Removal of Nano-Biothreats

Contamination of nano-biothreats, such as viruses, mycoplasmas, and pathogenic bacteria, is widespread in cell cultures and greatly threatens many cell-based bio-analysis and biomanufacturing. However, non-invasive trapping and removal of such biothreats during cell culturing, particularly many precious cells, is of great challenge. Here, inspired by the wake-riding effect, a biocompatible opto-hydrodynamic diatombot (OHD) based on optical trapping navigated rotational diatom (Phaeodactylum tricornutum Bohlin) for non-invasive trapping and removal of nano-biothreats is reported. Combining the opto-hydrodynamic effect and optical trapping, this rotational OHD enables the trapping of bio-targets down to sub-100 nm. Different nano-biothreats, such as adenoviruses, pathogenic bacteria, and mycoplasmas, are first demonstrated to be effectively trapped and removed by the OHD, without affecting culturing cells including precious cells such as hippocampal neurons. The removal efficiency is greatly enhanced via reconfigurable OHD array construction. Importantly, these OHDs show remarkable antibacterial capability, and further facilitate targeted gene delivery. This OHD serves as a smart micro-robotic platform for effective trapping and active removal of nano-biothreats in bio-microenvironments, and especially for cell culturing of many precious cells, with great promises for benefiting cell-based bio-analysis and biomanufacturing.

Direct ink writing 3D-printed optical waveguides for multi-layer interconnect

Low-cost, short-range optical interconnect technology plays an indispensable role in high-speed board-level data communications. In general, 3D printing technology can easily and quickly produce optical components with free-form shapes, while the traditional manufacturing process is complicated and time-consuming. Here, we present a direct ink writing 3D-printing technology to fabricate optical waveguides for optical interconnects. The waveguide core is 3D printed optical polymethylmethacrylate (PMMA) polymer, with propagation loss of 0.21 dB/cm at 980 nm, 0.42 dB/cm at 1310 nm, and 1.08 dB/cm at 1550 nm, respectively. Furthermore, a high-density multilayer waveguide arrays, including a four-layer waveguide arrays with a total of 144 waveguide channels, is demonstrated. Error-free data transmission at 30 Gb/s is achieved for each waveguide channel, indicating that the printing method can produce optical waveguides with excellent optical transmission performance. We believe this simple, low-cost, highly flexible, and environmentally friendly method has great potential for high-speed short-range optical interconnects.

On monocytes and lymphocytes biolens clustering by in flow holographic microscopy

Live cells act as biological lenses and can be employed as real-world optical components in bio-hybrid systems. Imaging at nanoscale, optical tweezers, lithography and also photonic waveguiding are some of the already proven functionalities, boosted by the advantage that cells are fully biocompatible for intra-body applications. So far, various cell types have been studied for this purpose, such as red blood cells, bacterial cells, stem cells and yeast cells. White Blood Cells (WBCs) play a very important role in the regulation of the human body activities and are usually monitored for assessing its health. WBCs can be considered bio-lenses but, to the best of our knowledge, characterization of their optical properties have not been investigated yet. Here, we report for the first time an accurate study of two model classes of WBCs (i.e., monocytes and lymphocytes) by means of a digital holographic microscope coupled with a microfluidic system, assuming WBCs bio-lens characteristics. Thus, quantitative phase maps for many WBCs have been retrieved in flow-cytometry (FC) by achieving a significant statistical analysis to prove the enhancement in differentiation among sphere-like bio-lenses according to their sizes (i.e., diameter d) exploiting intensity parameters of the modulated light in proximity of the cell optical axis. We show that the measure of the low intensity area (S: I z < I th z ) in a fixed plane, is a feasible parameter for cell clustering, while achieving robustness against experimental misalignments and allowing to adjust the measurement sensitivity in post-processing. 2D scatterplots of the identified parameters (d-S) show better differentiation respect to the 1D case. The results show that the optical focusing properties of WBCs allow the clustering of the two populations by means of a mere morphological analysis, thus leading to the new concept of cell-optical-fingerprint avoiding fluorescent dyes. This perspective can open new routes in biomedical sciences, such as the chance to find optical-biomarkers at single cell level for label-free diagnosis.

The Explanation of Photopic Luminous Efficiency Curve by Using Both of the Cones' Optical Fiber Coupling Effects and the Absorption of L Cones

In this paper, we build four-part cone models to explore the coupling effect of seven cone fiber couplers. Moreover, this is the first study of the coupling effect of four layers of biological couplers in animals and other biological lives. We simulate the four layers cone couplers by using the beam propagation method, and we assume the input beam is located at the outer fiber of the central cone. Our simulation results showed that there are two wavelength regions (short and long wavelength regions) with the strongest coupling, where the most power of input optical powers of the central cones will transfer to the six surrounding cones after transmitting through the four layers of cone couplers. However, within a wavelength region of ±75 nm near to the peak wavelengths, located in the yellow-green wavelength range, the splitting ratios at the output of the outer segment of the central cone are always greater than the sum of the splitting ratios of the six surrounding cones. These cone couplers may play an important role in color preprocessing (e.g., doing opponent color processing partially). The cone fiber coupler effect and light absorption of cones are considered separately in our models. By taking account of both the cone fiber coupling effect and absorption of outer segment of L cone, we find the multiplication of the relative optical power of cone couplers, the spectral sensitivity data of the L cone, and a normalized coefficient that matches with the photopic luminous efficiency of the human eye well. This is the attempt to use both the cone fiber coupling effect and the absorption of L cones to explain the photopic luminous efficiency. The splitting ratios of the central cones are greater than 80% at peak wavelengths located in the yellow-green wavelength range, and this can help to explain why the human eye is more sensitive to green light.

Investigation on the interaction mechanism of different SARS-CoV-2 spike variants with hACE2: insights from molecular dynamics simulations

Since the COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), SARS-CoV-2 has evolved by acquiring genomic mutations, resulting in the recent emergence of several SARS-CoV-2 variants with improved transmissibility and infectivity relative to the original strain. An underlying mechanism may be the increased ability of the mutants to bind the receptor proteins and infect the host cell. In this work, we implemented all-atom molecular dynamics (MD) simulations to study the binding and interaction of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein singly (D614G), doubly (D614G + L452R and D614G + N501Y), triply (D614G + N501Y + E484K), and quadruply (D614G + N501Y + E484K + K417T) mutated variants with the human angiotensin-converting enzyme 2 (hACE2) receptor protein in the host cell. A combination of multiple analysis approaches elucidated the effects of mutations and the extent of molecular divergence from multiple perspectives, including the dynamic correlated motions, interaction patterns, dominant motions, free energy landscape, and charge distribution on the electrostatic potential surface between the hACE2 and all RBD variants. Moreover, free energy calculations using the MM/PBSA method evaluated the binding affinity between these RBD variants and hACE2. The results showed that the D614G + N501Y + E484K variant possessed the lowest free energy value (highest affinity) compared to the D614G + N501Y + E484K + K417T, D614G + L452R, D614G + N501Y, and D614G mutants. The residue-based energy decomposition also indicated that the energy contribution of residues at the mutation site to the total binding energy was highly variable. The interaction mechanisms between the different RBD variants and hACE2 elucidated in this study will provide some insights into the development of drugs targeting the new SARS-CoV-2 variants.

Fluorescence inner filters of Arthrospira platensis: Novel perspective for precise fluorescence-based sensors

Microalgae have been reputed as novel biological materials due to their unique structure, surface functionality and optical activity, making them worthwhile agents in biosensing and theranostic applications. However, further scrutiny is required for utilizing them in routine optical techniques due to their complex structure and diverse chemical components. Here, laser induced fluorescence (LIF) features of a bio-compatible microalgae i. e. Arthrospira platensis (Spirulina) have been assessed. Typical fluorescence properties as well as the inner filter effects (IFEs) were examined and revealed to be strongly dependent on concentration, excitation wavelength, and detection geometry as well. IFEs and resulting spectral shifts have been analyzed considering various SP chromophores, reabsorption processes, and resonance energy transfer (RET) mainly from "Carotenoids to Phycobilisomes" as well as "Phycobilisomes to Chlorophyll-a". As a result, LIF spectral shift due to the re-absorption events (secondary-IFE) is introduced as a credible parameter for design of precise fluorescence-based sensors, due to being less dependent on ambient noises. We hope that the findings provide novel features regarding the LIF of Spirulina (SP) that could be utilized to design and develop optical sensors in the field of photonics, material diagnosis and biomedical theranostics.

Properties and Applications of Random Lasers as Emerging Light Sources and Optical Sensors: A Review

In a random laser (RL), optical feedback arises from multiple scattering instead of conventional mirrors. RLs generate a laser-like emission, and meanwhile take advantage of a simpler and more flexible laser configuration. The applicability of RLs as light sources and optical sensors has been proved. These applications have been extended to the biological field, with tissues as natural scattering materials. Herein, the current state of the RL properties and applications was reviewed.

Analysis of Polarization Images in the Microphysical Blood Parameters Research for the Hematocrit Diagnostics

The development of non-invasive optoelectronic technologies for human blood monitoring is one of the important research areas for medicine. A critical analysis of optoelectronic methods of blood research and the micromechanical systems based on them is carried out in this article. A design realization of a polarizing portable system for non-invasive monitoring of hematocrit as one of the basic homeostatic constants of the human body containing information about the microphysical parameters of blood cells has been substantiated. A physical model of polarized radiation conversion in a video information system of laser sensing of a biological research object has been formed. Visual and quantitative differences in the spatial distribution of polarization parameters of the scattered radiation for the states of the body with different hematocrit levels have been revealed. A scheme of a multichannel imaging portable system, based on a smartphone using miniature optical and microelectronic components of information conversion for non-invasive monitoring of microphysical blood parameters, has been created. The system implements the principle of polarimetric blood photometry and a multiparametric analysis of the polarization properties of the laser radiation scattered by blood. The developed portable optoelectronic system, based on a smartphone, can be used for rapid blood diagnostics in disaster medicine and the presence of clinical contraindications to the formation of invasive tests. The proposed polarization-based approach is a promising automated alternative to traditional devices and systems for the research of microphysical blood parameters.

Geometry design for a fully insertable glucose biosensor with multimodal optical readout

Significance

Insertable optical continuous glucose monitors (CGMs) with wearable readers are a strong option for monitoring individuals with diabetes. However, a fully insertable CGM requires a small form factor while still delivering sufficient signal to be read through tissue by an external device. Previous work has suggested that a multimodal repeating unit (barcode) approach may meet these requirements, but the biosensor geometry must be optimized to meet performance criteria.

Aim

This work details in silico trials conducted to evaluate the geometry of a fully insertable multimodal optical biosensor with respect to both optical output and species diffusion in vivo.

Approach

Monte Carlo modeling is used to evaluate the luminescent output of three presupposed biosensor designs based on size constraints for an injectable and logical placement of the bar code compartments. Specifically, the sensitivity of the luminescent output to displacement of the biosensor in the X and Y directions, overall size of the selected design, and size of an individual repeating unit are analyzed. Further, an experimentally validated multiphysics model is used to evaluate the diffusion and reaction of glucose and oxygen within the biosensor to estimate the occurrence of chemical crosstalk between the assay components.

Results

A stacked cylinder multimodal biosensor 4.4 mm in length with repeating units 0.36 mm in length was found to yield a greater luminescent output than the current "barcode" biosensor design. In addition, it was found that a biosensor with enzymatic elements does not significantly deplete glucose locally and thus does not impact the diffusion profile of glucose in adjacent compartments containing nonenzymatic assays.

Conclusions

Computational modeling was used to design the geometry of a multimodal, insertable, and optical CGM to ensure that the optical output and chemical diffusion profile are sufficient for this device to function in vivo.

Motor-like microlasers functioning in biological fluids

Microlasers integrated with biological systems have received tremendous attention for their intense light intensity and narrow linewidth recently, serving as a powerful tool for studying complex dynamics and interactions in scattered biological micro-environments. However, manipulation of microlasers with controllable motions and versatile functions remains elusive. Herein, we introduce the concept of motor-like microlasers formed by magnetic-doped liquid crystal droplets, in which the direction and velocity could be controlled by altering internal magnetic nanoparticles or external magnetic fields. Both translational and rotatory motions of the lasing resonator could be continually changed in real-time. Lasing-encoded motors carrying different functions and lasing wavelengths were also achieved. Finally, we demonstrate the potential of motor-like microlasers by functioning as a localized stimulation emission light source to stimulate or illuminate living cells, providing a novel approach for switching on/off light emissions and subcellular imaging. Laser emitting micromotors offer a facile system for precise manipulation of microlasers in biological fluids, providing new insight into the development of programmable on-chip laser devices and laser-emitting intelligent systems.

Computational Design of Miniprotein Inhibitors Targeting SARS-CoV-2 Spike Protein

The ongoing pandemic of COVID-19 caused by SARS-CoV-2 has become a global health problem. There is an urgent need to develop therapeutic drugs, effective therapies, and vaccines to prevent the spread of the virus. The virus first enters the host cell through the interaction between the receptor binding domain (RBD) of spike protein and the peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2). Therefore, blocking the binding of RBD and ACE2 is a promising strategy to inhibit the invasion and infection of the virus in the host cell. In the study, we designed several miniprotein inhibitors against SARS-CoV-2 by single/double/triple-point mutant, based on the initial inhibitor LCB3. Molecular dynamics (MD) simulations and trajectory analysis were performed for an in-depth analysis of the structural stability, essential protein motions, and per-residue energy decomposition involved in the interaction of inhibitors with the RBD. The results showed that the inhibitors have adapted the protein RBD in the binding interface, thereby forming stable complexes. These inhibitors display low binding free energy in the MM/PBSA calculations, substantiating their strong interaction with RBD. Moreover, the binding affinity of the best miniprotein inhibitor, H6Y-M7L-L17F mutant, to RBD was ∼45 980 times (ΔG = RT ln Ki) higher than that of the initial inhibitor LCB3. Following H6Y-M7L-L17F mutant, the inhibitors with strong binding activity are successively H6Y-L17F, L17F, H6Y, and F30Y mutants. Our research proves that the miniprotein inhibitors can maintain their secondary structure and have a highly stable blocking (binding) effect on SARS-CoV-2. This study proposes novel miniprotein mutant inhibitors with enhanced binding to spike protein and provides potential guidance for the rational design of new SARS-CoV-2 spike protein inhibitors.

Calibration Methods of a Portable Polarizing System for Monitoring Optically Inhomogeneous Media

Theoretical aspects of methods for calibrating Stokes polarimeters are considered. The prospects and opportunities for implementing the presented methods for calibrating portable polarization systems used in biology and medicine are determined. Based on a comparative analysis, a method for calibrating a portable Stokes polarimeter for medical applications is proposed. The chosen method provides the smallest error in measuring the parameters of the Stokes vector for calculating the parameters of optical anisotropy and researching the polarization properties of biological tissues. A series of experimental research and statistical analysis of the spatial distributions of the polarization parameters of the calibration sample was carried out to use the results for forming the instrument matrix of the developed Stokes polarimeter during calibration.

Molecular Dynamics Simulation Investigation of the Binding and Interaction of the EphA6-Odin Protein Complex

Protein-protein interaction plays an important role in the development of almost all cells. Elucidating the dynamic binding and affinity of a protein-protein complex is essential for understanding the biological functions of proteins. EphA6 and Odin proteins are members of the Eph (erythropoietin-producing hepatocyte) receptor family and the Anks (ankyrin repeat and sterile α motif domain-containing) family, respectively. Odin significantly functions in regulating endocytosis, degradation, and stability of EphA receptors. In this work, the key residues of the interaction interface were determined through a hydrogen bond, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and dynamic correlation analysis of the conventional molecular dynamics (MD) simulations. The calculated standard binding free energy, -7.92 kcal/mol, between EphA6 and Odin is quite consistent with the experimental measurement value, -8.73 kcal/mol. By the combination of several MD simulation techniques, our investigation of the binding process reveals the detailed representative characteristics of the entire binding pathway at the molecular level. Based on the obtained potential of the mean force (PMF) curve, the analysis of the simulation trajectories shows that the residue Arg1013 in the receptor EphA6 is responsible for capturing Asp739 and Asp740 in the ligand Odin during the initial stage of binding. In the later stage of binding, the hydrogen bonds and salt bridges between a series of residues Lys973, Leu1007, Gly1009, His1010, and Arg1012 in the receptor and residues Leu735, Asn736, Asp739, Asp740, and Asp753 in the ligand mainly contribute to the stability of the protein complex. In addition, the specific change process of the receptor-ligand-binding mode is also clarified during the binding process. Our present simulation will promote a deep understanding of the protein-protein interaction, and the identified key interresidue interaction will be theoretical guidance for the design of protein drugs.

Thermal-mechanical-photo-activation effect on silica micro/nanofiber surfaces: origination, reparation and utilization

The exploration relevant to the surface changes on optical micro- and nanofibers (MNFs) is still in infancy, and the reported original mechanisms remain long-standing puzzles. Here, by recognizing the combined interactions between fiber heating, mechanically tapering, and high-power pulsed laser guiding processes in MNFs, we establish a general thermal-mechanical-photo-activation mechanism that can explain the surface changes on MNFs. Our proposed activation mechanism can be well supported by the systematical experimental results using high-intensity nanosecond/femtosecond pulsed lasers. Especially we find large bump-like nanoscale cavities on the fracture ends of thin MNFs. Theoretically, on the basis of greatly increased bond energy activated by the fiber heating and mechanically tapering processes, the energy needed to break the silicon-oxygen bond into dangling bonds is significantly reduced from its intrinsic bandgap of ∼9 eV to as low as ∼4.0 eV, thus high-power pulsed lasers with much smaller photon energy can induce obvious surface changes on MNFs via multi-photon absorption. Finally, we demonstrate that using surfactants can repair the MNF surfaces and exploit them in promising applications ranging from sensing and optoelectronics to nonlinear optics. Our results pave the way for future preventing the performances from degradation and enabling the practical MNF-based device applications.

A nanotheranostic agent based on Nd3+-doped YVO4 with blood-brain-barrier permeability for NIR-II fluorescence imaging/magnetic resonance imaging and boosted sonodynamic therapy of orthotopic glioma

The specific diagnosis and treatment of gliomas is a primary challenge in clinic due to their high invasiveness and blood-brain barrier (BBB) obstruction. It is highly desirable to find a multifunctional agent with good BBB penetration for precise theranostics. Herein, we design and construct a core-shell structured nanotheranostic agent (YVO₄:Nd³⁺-HMME@MnO₂-LF, marked as YHM) with YVO₄:Nd³⁺ particles as the core and MnO₂ nanosheets as the shell. Sonosensitizer hematoporphyrinmonomethyl ether (HMME) and lactoferrin (LF) were further loaded and modified on the surface, giving it a good ability to cross the BBB, near-infrared fluorescence imaging in the second window (NIR-II)/magnetic resonance imaging (MRI) bimodality, and highly efficient sonodynamic therapy (SDT) of orthotopic gliomas. The YVO₄:Nd³⁺ (25%) core exhibited good NIR-II fluorescence properties, enabling YHM to act as promising probes for NIR-II fluorescence imaging of vessels and orthotopic gliomas. MnO₂ shell can not only provide O₂ in the tumor microenvironments (TME) to significantly improve the healing efficacy of SDT, but also release Mn²⁺ ions to achieve T₁-weight MRI in situ. Non-invasive SDT can effectively restrain tumor growth. This work not only demonstrates that multifunctional YHM is promising for diagnosis and treatment of orthotopic glioma, but also provides insights into exploring the theranostic agents based on rare earth-doped yttrium vanadate nanoparticles.

Cellular lasers for cell imaging and biosensing

The possibility to produce laser action involving biomaterials, in particular (single) biological cells, has fostered the development of cellular lasers as a novel approach in biophotonics. In this respect, cells that are engineered to carry gain medium (e.g., fluorescent dyes or proteins) are placed inside an optical cavity (i.e., typically a sandwich of highly reflective mirrors), allowing the generation of stimulated emission upon sufficient optical pumping. In another scenario, micron-sized optical resonators supporting whispering-gallery mode (WGM) or semiconductor-based laser probes can be internalized by the cells and support light amplification. This review summarizes the recent advances in the fields of biolasers and cellular lasers, and most importantly, highlights their potential applications in the fields of in vitro and in vivo cell imaging and analysis. They include biosensing (e.g., in vitro detection of sodium chloride (NaCl) concentration), cancer cell imaging, laser-emission-based microscope, cell tracking, cell distinction study, and tissue contraction monitoring in zebrafish. Lastly, several fundamental issues in developing cellular lasers including laser probe fabrication, biocompatibility of the system, and alteration of local refractive index of optical cavities due to protein absorption or probe aggregation are described. Cellular lasers are foreseen as a promising tool to study numerous biological and biophysical phenomena. STATEMENT OF SIGNIFICANCE: Biolasers are generation of laser involving biological materials. Biomaterials, including single cells, can be engineered to incorporate laser probes or fluorescent proteins or fluorophores, and the resulting light emission can be coupled to optical resonator, allowing generation of cellular laser emission upon optical pumping. Unlike fluorescence, this stimulated emission is very sensitive and is capable of detecting small alterations in the optical property of the cells and their environment. In this review, recent development and applications of cellular lasers in the fields of in vitro and in vivo cell imaging, cell tracking, biosensing, and cell/tissue analysis are highlighted. Several challenges in developing cellular lasers including probe fabrication and biocompatibility as well as alteration of cellular environment are explained.

Optical van-der-Waals forces in molecules: from electronic Bethe-Salpeter calculations to the many-body dispersion model

Molecular forces induced by optical excitations are connected to a wide range of phenomena, from chemical bond dissociation to intricate biological processes that underpin vision. Commonly, the description of optical excitations requires the solution of computationally demanding electronic Bethe-Salpeter equation (BSE). However, when studying non-covalent interactions in large-scale systems, more efficient methods are desirable. Here we introduce an effective approach based on coupled quantum Drude oscillators (cQDO) as represented by the many-body dispersion model. We find that the cQDO Hamiltonian yields semi-quantitative agreement with BSE calculations and that both attractive and repulsive optical van der Waals (vdW) forces can be induced by light. These optical-vdW interactions dominate over vdW dispersion in the long-distance regime, showing a complexity that grows with system size. Evidence of highly non-local forces in the human formaldehyde dehydrogenase 1MC5 protein suggests the ability to selectively activate collective molecular vibrations by photoabsorption, in agreement with recent experiments.

The authors devise an efficient quantum approach to address the van der Waals interactions due to photoexcitations by approximating the Bethe-Salpeter equation. Both attractive/repulsive forces can arise, that could couple to collective protein dynamics.

Polarisation optics for biomedical and clinical applications: a review

Many polarisation techniques have been harnessed for decades in biological and clinical research, each based upon measurement of the vectorial properties of light or the vectorial transformations imposed on light by objects. Various advanced vector measurement/sensing techniques, physical interpretation methods, and approaches to analyse biomedically relevant information have been developed and harnessed. In this review, we focus mainly on summarising methodologies and applications related to tissue polarimetry, with an emphasis on the adoption of the Stokes-Mueller formalism. Several recent breakthroughs, development trends, and potential multimodal uses in conjunction with other techniques are also presented. The primary goal of the review is to give the reader a general overview in the use of vectorial information that can be obtained by polarisation optics for applications in biomedical and clinical research.

Ultrasensitive detection of endocrine disruptors via superfine plasmonic spectral combs

The apparent increase in hormone-induced cancers and disorders of the reproductive tract has led to a growing demand for new technologies capable of detecting endocrine disruptors. However, a long-lasting challenge unaddressed is how to achieve ultrahigh sensitive, continuous, and in situ measurement with a portable device for in-field and remote environmental monitoring. Here we demonstrate a simple-to-implement plasmonic optical fiber biosensing platform to achieve an improved light-matter interaction and advanced surface chemistry for ultrasensitive detection of endocrine disruptors. Our platform is based on a gold-coated highly tilted fiber Bragg grating that excites high-density narrow cladding mode spectral combs that overlap with the broad absorption of the surface plasmon for high accuracy interrogation, hence enabling the ultrasensitive monitoring of refractive index changes at the fiber surface. Through the use of estrogen receptors as the model, we design an estradiol-streptavidin conjugate with the assistance of molecular dynamics, converting the specific recognition of environmental estrogens (EEs) by estrogen receptor into surface-based affinity bioassay for protein. The ultrasensitive platform with conjugate-induced amplification biosensing approach enables the subsequent detection for EEs down to 1.5 × 10^-3 ng ml^-1 estradiol equivalent concentration level, which is one order lower than the defined maximal E₂ level in drinking water set by the Japanese government. The capability to detect EEs down to nanogram per liter level is the lowest limit of detection for any estrogen receptor-based detection reported thus far. Its compact size, flexible shape, and remote operation capability open the way for detecting other endocrine disruptors with ultrahigh sensitivity and in various hard-to-reach spaces, thereby having the potential to revolutionize environment and health monitoring.

Light-Harvesting in Biophotonic Optofluidic Microcavities via Whispering-Gallery Modes

Phycobiliproteins are a class of light-harvesting fluorescent proteins existing in cyanobacteria and microalgae, which harvest light and convert it into electricity. Owing to recent demands on environmental-friendly and renewable apparatuses, phycobiliproteins have attracted substantial interest in bioenergy and sustainable devices. However, converting energy from biological materials remains challenging to date. Herein, we report a novel scheme to enhance biological light-harvesting through light-matter interactions at the biointerface of whispering-gallery modes (WGMs), where phycobiliproteins were employed as the active gain material. By exploiting microdroplets as a carrier for light-harvesting biomaterials, strong local electric field enhancement and photon confinement at the cavity interface resulted in significantly enhanced bio-photoelectricity. A threshold-like behavior was discovered in photocurrent enhancement and the WGM modulated fluorescence. Systematic studies of biologically produced photoelectricity and optical mode resonance were carried out to illustrate the impact of the cavity quality factor, structural geometry, and refractive indices. Finally, a biomimetic system was investigated by exploiting cascade energy transfer in phycobiliprotein assembly composed of three light-harvesting proteins. The key findings not only highlight the critical role of optical cavity in light-harvesting but also offer deep insights into light energy coupling in biomaterials.